Contacts of the helix formed by residues 418 - 425 (chain B) in PDB entry 3NA0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 418 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B HIS* 4.3 17.0 - - + +
82B PHE* 3.4 33.4 - - + -
100B TYR* 5.1 4.0 - - + -
101B VAL 3.0 13.2 + - - +
102B ILE* 4.6 1.5 - - + +
392B VAL 4.0 4.9 - - - -
393B THR* 4.1 5.8 - - + -
416B GLN 3.7 1.6 + - - -
417B VAL* 1.3 68.2 - - - +
419B ILE* 1.3 54.6 + - - +
420B TYR 3.2 3.1 - - - -
421B ALA* 3.0 9.3 + - + -
422B LEU* 2.8 34.1 + - - +
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Residues in contact with ILE 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B LEU 5.2 2.7 - - - +
386B ARG 4.7 2.6 - - - +
389B PRO* 3.4 19.7 - - + -
391B SER* 3.3 22.4 - - - +
392B VAL 3.2 7.3 + - - +
393B THR* 4.4 2.0 - - - -
394B LEU* 3.7 25.6 - - + -
417B VAL* 2.8 40.7 + - + +
418B ALA* 1.3 71.0 - - - +
420B TYR* 1.3 63.6 + - - +
422B LEU* 3.4 7.8 - - + +
423B GLY* 3.2 19.1 + - - -
453B LEU* 3.6 37.5 - - + +
454B GLY* 5.3 6.5 - - - -
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Residues in contact with TYR 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B HIS* 3.6 51.8 - + + -
76B LEU* 4.5 8.9 - - + +
78B HIS* 5.8 1.8 - - - +
79B VAL* 4.0 13.5 - - + -
386B ARG 4.8 1.1 - - - +
387B LEU 4.1 2.0 - - - -
388B HIS* 5.6 0.4 - - - -
389B PRO* 3.9 24.2 - - + -
392B VAL* 3.2 16.0 + - + +
419B ILE* 1.3 77.1 - - - +
421B ALA* 1.3 67.7 + - - +
423B GLY* 3.4 9.9 + - - -
424B ARG* 3.3 67.0 + - + +
495B THR* 4.3 13.1 + - + -
501B LEU* 3.9 19.7 - - + -
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Residues in contact with ALA 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B HIS* 4.4 3.5 + - + +
79B VAL* 4.0 29.3 - - + +
82B PHE* 4.1 9.9 - - + -
102B ILE* 3.7 16.9 - - + +
418B ALA* 3.0 20.5 + - + +
420B TYR* 1.3 79.6 - - - +
422B LEU* 1.3 65.9 + - - +
424B ARG* 3.1 4.3 + - - +
425B GLU* 3.1 23.9 + - - +
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Residues in contact with LEU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ILE* 3.7 34.8 - - + +
104B PRO* 4.0 10.3 - - + -
107B VAL* 4.9 2.0 - - + -
417B VAL* 4.8 9.0 - - + -
418B ALA 2.8 16.6 + - - +
419B ILE* 3.4 9.6 - - + +
421B ALA* 1.3 75.2 - - - +
423B GLY* 1.3 57.5 + - - +
425B GLU* 3.0 22.9 + - - +
428B PHE* 3.7 28.5 - - + -
429B PHE* 3.6 19.8 - - + -
450B PHE 4.3 8.1 - - - +
451B ARG* 5.2 4.5 - - - +
453B LEU* 3.8 28.5 - - + -
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Residues in contact with GLY 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B ARG* 2.6 54.2 + - - +
387B LEU* 4.7 0.2 - - - +
419B ILE 3.2 8.4 + - - -
420B TYR 3.4 1.7 + - - -
421B ALA 3.3 0.6 - - - -
422B LEU* 1.3 78.0 - - - +
424B ARG* 1.3 65.7 + - - +
425B GLU 3.4 0.2 - - - -
429B PHE* 3.8 15.8 - - - -
432B PRO* 3.7 2.6 - - - +
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Residues in contact with ARG 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B VAL* 5.2 7.6 - - + -
386B ARG 4.9 0.2 + - - -
387B LEU* 2.6 52.4 + - - +
388B HIS* 3.9 15.4 + - - -
420B TYR* 3.3 58.2 + - + +
421B ALA* 3.1 8.7 + - - +
423B GLY* 1.3 82.9 - - - +
425B GLU* 1.3 59.1 + - - +
426B PRO* 3.3 13.9 - - - +
432B PRO* 3.5 15.6 - - - +
433B GLU* 5.5 13.5 + - + +
495B THR* 4.3 5.1 + - - -
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Residues in contact with GLU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE* 6.1 1.0 - - - +
83B GLN* 5.8 4.9 + - - +
102B ILE* 4.1 13.0 - - + +
421B ALA 3.1 11.2 + - - +
422B LEU 3.0 16.6 + - - +
423B GLY 3.4 0.2 - - - -
424B ARG* 1.3 75.7 - - - +
426B PRO* 1.4 71.3 - - - +
427B THR* 2.7 44.7 + - - +
428B PHE* 3.0 38.7 + - + -
429B PHE* 3.2 12.8 + - - +
432B PRO* 4.1 1.3 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il